Spiophanes bombyx (Claparède, 1870) from the Gulf of Naples, Tyrrhenian Sea, Italy, was the first described Spiophanes with fronto-lateral horns on the prostomium. It was also considered the only horned species occurring in European waters. Our sequence data of five gene fragments suggest the presence of two horned sibling Spiophanes species in northern Europe: S. cf. bombyx in the North and the Norwegian seas, and S. cf. convexus in Brittany, northern France, and Bay of Biscay, northern Spain. Spiophanes cf. bombyx worms are genetically close to a single examined specimen of S. bombyx from Venice Lagoon, Italy but their conspecificity should be verified by further study. Our sequence data show that horned Spiophanes from the North Pacific are genetically distant from horned European species, and that S. uschakowi Zachs, 1933, originally described from the Sea of Japan (East Sea) is a valid species. The data also suggest the presence of two horned sibling Spiophanes species in the North East Pacific: S. hakaiensis Radashevsky & Pankova, n. sp. distributed from Alaska south to about Point Conception, and S. norrisi Meißner & Blank, 2009, distributed from San Francisco Bay south to Baja California Sur, Mexico. Spiophanes from South America, morphologically similar to S. norrisi, are suggested to belong to a new species. Molecular data also suggest the presence of two sibling species among the worms from northern Europe identified by morphology as S. kroyeri Grube, 1860. Worms from the Barents Sea and northern part of the North Sea are tentatively referred to as S. cf. kroyeri; worms from the northern and central parts of the North Sea and from the Bay of Biscay, northern Spain, are tentatively referred to as S. cf. cirrata M. Sars in G.O. Sars, 1872. Sequence data also show that S. duplex from California is genetically different from morphologically similar worms from South America. The South American worms are referred to resurrected S. soederstroemi Hartman, 1953 which was originally described from off Rio Grande do Sul, Brazil, and then considered as a junior synonym of S. duplex. Analysis of divergence times of Spiophanes lineages suggested that the origin of the most recent common ancestor of horned Spiophanes with metameric nuchal organs was around 11.1 mya (95% HPD: 5.1–19.0 mya) and that the divergence of the North Atlantic and North Pacific lineages was around 7.9 mya (95% HPD: 4.1–13.3 mya). The North Atlantic lineage was estimated to have diverged 4.8 mya (95% HPD: 2.2–8.6 mya), resulting in the origin of S. cf. bombyx and S. cf. convexus. The North Pacific lineage was estimated to have diverged first by the isolation and speciation of S. norrisi 1.7 mya (95% HPD: 2.3–1.0 mya), and then by the isolation and speciation of S. uschakowi and S. hakaiensis n. sp. 1.3 mya (95% HPD: 2.0–0.7 mya). The estimates place the divergences soon after maximum glacial period in the North Pacific (2.4–3.0 mya).